There are more specific cases where open source tooling outperforms Mathematica than where the opposite holds. This especially true when you move away from basic calculus and towards research math. For example, many number theorists don't care about Mathematica at all because it has virtually no functionality for modular forms and L-functions which Pari/GP and Sage on the other hand support very well.

However, nothing open source currently comes close to Mathematica for symbolic and symbolic-numerical calculus (expression simplification, symbolic integration, solving PDEs, etc.). Also, one of Mathematica's main strengths is providing a lot of functionality in a neat package where diverse components are very easy for the user to glue together, with automagical interfaces where the user doesn't need to know what happens behind the scenes (or at least that's how Wolfram PR spins Mathematica being closed source).

Meanwhile, Sage combines a lot of functionality but you can't go very far before you run into visible duct tape, API inconsistencies and things that don't quite work together automatically when you think they ought to. Its documentation is also not as good (Sage has very detailed documentation, but often not well structured). Many of the same issues that exist in open source software in other fields, really.